Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method

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dc.contributor.authorKenta, T.
dc.contributor.authorGratten, J.
dc.contributor.authorWatson-Haigh, N.
dc.contributor.authorHinten, G.
dc.contributor.authorSlate, J.
dc.contributor.authorButlin, R.
dc.contributor.authorBurke, T.
dc.date.issued2008
dc.description.abstractWe describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.
dc.description.statementofresponsibilityT. Kenta, J. Gratten, N. S. Haigh, G. N. Hinten, J. Slate, R. K. Butlin, and T. Burke
dc.identifier.citationMolecular Ecology Resources, 2008; 8(6):1230-1238
dc.identifier.doi10.1111/j.1755-0998.2008.02190.x
dc.identifier.issn1755-098X
dc.identifier.issn1755-0998
dc.identifier.orcidWatson-Haigh, N. [0000-0002-7935-6151]
dc.identifier.urihttp://hdl.handle.net/2440/86921
dc.language.isoen
dc.publisherBlackwell Publishing
dc.rights© 2008 The Authors
dc.source.urihttps://doi.org/10.1111/j.1755-0998.2008.02190.x
dc.subjectgenotyping; locked nucleic acid (LNA); medium throughput; nonmodel organism; single nucleotide polymorphism (SNP); small reaction scale; universal fluorescent-labelled oligonucleotide (UFO) primer
dc.titleMultiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method
dc.typeJournal article
pubs.publication-statusPublished

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